What does the gamma p-value represent? How is it different from the p-value for each pathway?
Pathway-Express provides two types of p-values for each pathway: i) p-value obtained using the classical statistics (referred to as classical p-value) and ii) p-value obtained using the impact analysis (referred to as gamma p-value). This classical p-value appears in the first term in Equation 1 (see paper). It can be obtained using hypergeometric, binomial or any other appropriate statistical distribution. The corrected p-value is the classical p-value corrected for multiple comparisons. The gamma p-value is the p-value provided by the impact analysis as described in the paper. This is the p-value that one should look at. However, note that there is a tendency to include some false positives if the list of input genes is very small, as discussed briefly in the supplementary materials. Pathway-Express provides both p-values in order to allow comparison of the results of the classical approach with the results of the impact analysis.
